lab3d

CellSim Lab

A biology lab you walk into in first person. Prepare slides of onion skin, cheek cells or a pondweed leaf, then focus a microscope on them. Or grow living A549 lung cancer cells, treat them with a drug and incubate them. The living cells are simulated by the Cell Sim engine (cellsim.cell.dish), running in the browser.

Run it

Browsers block 3D models and the engine on pages opened straight from a file, so serve the web folder:

cd "Cell Sim/web"
python3 -m http.server 8000

Then open http://localhost:8000/lab3d/.

The engine uses the wheel in ../lab/wheel/ (the same one the Lab page uses). GitHub Pages builds it on every deploy. To build it locally:

cd "Cell Sim"
python -m pip wheel --no-deps --no-build-isolation -w web/lab/wheel .
cd web/lab/wheel && ls -t cellsim-*-py3-none-any.whl | head -1 > LATEST

The first time you look at a culture dish, the browser downloads Python (Pyodide, about 30 s). After that it is cached.

Controls

Key	Does
W A S D, mouse	Walk, look
Left click	Take the thing you look at into your pocket
Right click	Use or open the thing you look at; with an item in hand, use it on what you look at, or put it down
Hold right click	Lower a cover slip slowly (a quick tap drops it flat and traps air)
1–9, scroll	Pick a hotbar slot
Q	Put down the item in your hand
E	Inventory
J	Lab journal
Space, Shift, Ctrl	Jump, sneak, sprint
Esc	Pause
F3	Frame rate, draw calls and memory

The experiments

• Onion skin cells: goggles, wash your hands, slide on the white tile, cut the onion with the scalpel, peel the skin with the forceps, one drop of iodine, cover slip, stage, then focus at 4×, 10× and 40×.
• Your cheek cells: swab your cheek, smear it on the slide, put the swab in the disinfectant, then add methylene blue.
• Pondweed leaf cells: a drop of water first, then one leaf from the tank. At 400× the chloroplasts stream around each cell.
• Living cancer cells: take Dish A from the incubator and look at it, add drops of paclitaxel, doxorubicin or cisplatin, incubate, and compare with Dish B, the untreated control. The doses are real dilutions: two 50 µL drops of 10 µM paclitaxel in 5.1 mL of medium give 0.196 µM. The engine's cell counts appear in the journal.

Graphics and battery

Settings → Graphics: Auto picks a preset from the graphics chip.

Preset	Detail
Low	Older Macs and laptops on battery: 0.75× resolution, no shadows, no smoothing, one ceiling lamp, 30 fps
Medium	Shadows from the windows, two lamps
High	Sharper shadows, four lamps
Ultra	Full resolution, 4096 px shadows, all six lamps, no frame cap

The game stops drawing when nothing moves, and the Cell Sim engine (about 150 MB of memory) only loads once a culture dish needs it.

What's where

Path
index.html, css/game.css	Screens and HUD
js/main.js	Game loop, input, inventory, the microscope stage, incubator and drawers
js/room.js	The room, furniture, lights and colliders
js/items.js	Every item and what left- and right-click do with it
js/props.js	Equipment built in code: slides, bottles, beakers, dishes, the pondweed tank, tools
js/liquids.js	Volumes, colour mixing and drug dilution
js/scope.js, js/specimens.js, js/culture.js	The view through the eyepiece
js/engine.js, js/engine-worker.js, js/lab_engine.py	The Cell Sim engine, in a background worker
js/tasks.js, js/journal.js	Experiments and the lab journal
assets/	Models, textures and lighting (downloads/ holds the raw Sketchfab files and is not committed)

Honest notes

• The living cells are the engine's: positions, cell-cycle phase, p53, caspase-3 and DNA damage come from run_dish_stream. Only their outlines are drawn here.
• The onion, cheek and pondweed slides are drawn at measured cell sizes. They are not simulated.

Credits

• Cell engine: Cell Sim (MIT), in the browser via Pyodide.
• 3D engine: three.js r160 (MIT).
• Poly Haven (CC0): yellow onion, metal stool, steel shelves, fluorescent lights, drawer cabinet, clipboard, stationery, wall clock, magnifying glass, binder notebook, metal office desk, floor tiles, painted plaster, and the hospital room HDRI.
• Sketchfab (CC Attribution 4.0):
  • Chemistry Lab Table by Jawahar Yokesh
  • lab bench by Konstantin_Keller (the incubator)
  • Compound Microscope by kg007
  • Door Classroom by Mehdi Shahsavan
• Built in code: the room, slides, cover slips, bottles, beakers, culture dishes, the pondweed tank, the lab tools, the safety goggles, the hand sanitizer and the window blinds.